[English] 日本語
Yorodumi
- PDB-2vve: Crystal structure of the stem and receptor binding domain of the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vve
TitleCrystal structure of the stem and receptor binding domain of the spike protein P1 from bacteriophage PM2
ComponentsSPIKE PROTEIN P1
KeywordsVIRAL PROTEIN / VIRAL STEM-RECEPTOR BINDING DOMAIN
Function / homology
Function and homology information


Jelly Rolls - #770 / Jelly Rolls - #720 / Phage PM2 spike protein P1 / Spike protein P1, first jelly-roll domain / Spike protein P1, second jelly-roll domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPSEUDOALTEROMONAS PHAGE PM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsAbrescia, N.G.A. / Grimes, J.M. / Kivela, H.K. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I.
CitationJournal: Mol.Cell / Year: 2008
Title: Insights Into Virus Evolution and Membrane Biogenesis from the Structure of the Marine Lipid-Containing Bacteriophage Pm2.
Authors: Abrescia, N.G.A. / Grimes, J.M. / Kivela, H.K. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I.
History
DepositionJun 6, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SPIKE PROTEIN P1
B: SPIKE PROTEIN P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3797
Polymers57,1832
Non-polymers1965
Water9,710539
1
A: SPIKE PROTEIN P1
hetero molecules

A: SPIKE PROTEIN P1
hetero molecules

A: SPIKE PROTEIN P1
hetero molecules

A: SPIKE PROTEIN P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,66812
Polymers114,3664
Non-polymers3028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8570 Å2
ΔGint-15.8 kcal/mol
Surface area53000 Å2
MethodPQS
2
B: SPIKE PROTEIN P1
hetero molecules

B: SPIKE PROTEIN P1
hetero molecules

B: SPIKE PROTEIN P1
hetero molecules

B: SPIKE PROTEIN P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,84716
Polymers114,3664
Non-polymers48112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area8380 Å2
ΔGint-17.5 kcal/mol
Surface area54040 Å2
MethodPQS
Unit cell
Length a, b, c (Å)107.894, 107.894, 44.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-2063-

HOH

21B-2048-

HOH

31B-2067-

HOH

-
Components

#1: Protein SPIKE PROTEIN P1 / P1-RECEPTOR BINDING PROTEIN


Mass: 28591.408 Da / Num. of mol.: 2 / Fragment: STEM-RECEPTOR BINDING DOMAIN, RESIDUES 82-335
Source method: isolated from a genetically manipulated source
Details: CLONED FRAGMENT STARTS AT RESIDUE 82 AND STOPS AT RESIDUE 335
Source: (gene. exp.) PSEUDOALTEROMONAS PHAGE PM2 (virus) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9XJR3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.4 %
Description: THE ELECTRON DENSITY MAP FOR THE STEM DOMAIN WAS GREATLY IMPROVED BY USING BUSTER PROGRAM IN THE EARLY REFINEMENT CYCLES
Crystal growpH: 8
Details: 7.3MG/ML (IN 150MM NACL, 20MM TRIS PH 7.5, 10MM CACL2),20%(W/V) PEG6K,100MM TRIS PH 8, 200MM LICL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9185
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 30, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 1.77→23 Å / Num. obs: 47548 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.2
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.8 / % possible all: 71.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VVD

2vvd


Resolution: 1.77→23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.082 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DESPITE HAVING TWO MOLECULES IN THE ASU THE RESPECTIVE STEM DOMAINS FLEX WITH DIFFERENT ANGLES RELATIVE TO THE RECEPTOR DOMAIN. THEREFORE NO STRICT NCS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2423 5.1 %RANDOM
Rwork0.173 ---
obs0.176 45122 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.77→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 5 539 4510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9455555
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25824.471208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52215655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6371526
X-RAY DIFFRACTIONr_chiral_restr0.0750.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023188
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.21676
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22791
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.2125
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.807102571
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.732204076
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.045201705
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.438401473
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.81 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 110
Rwork0.242 2426
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.97860.06610.22320.7189-0.130.71430.0141-0.00360.09650.0875-0.0403-0.058-0.10450.0320.02620.064-0.012-0.02770.03340.00150.0176.86314.60233.952
22.17830.0965-0.06471.1830.1522.0860.0097-0.09220.2094-0.1157-0.0398-0.0801-0.06430.03330.03010.04530.00270.00490.0047-0.00710.01043.62136.0161.707
30.14320.4829-0.24482.0789-1.7142.17060.0039-0.0162-0.03150.1232-0.0809-0.1074-0.15030.04930.0770.03480.0151-0.0170.04670.00460.01154.15327.4119.345
40.9512-0.35060.30270.7669-0.32290.81-0.00120.05440.02650.0527-0.0262-0.17010.05410.15170.02740.04110.0012-0.00680.07390.01340.0159-37.89251.191-25.082
52.13680.60331.21122.33672.06563.3545-0.0188-0.30490.1087-0.0057-0.16740.1375-0.071-0.42360.1862-0.00780.0453-0.0160.0833-0.05-0.0388-21.2340.446.963
61.52670.15611.13990.01730.08861.4482-0.135-0.14030.20360.0005-0.0076-0.0078-0.1525-0.04490.14270.05590.0433-0.03020.0842-0.05550.0061-22.10342.5591.86
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A84 - 168
2X-RAY DIFFRACTION2A169 - 306
3X-RAY DIFFRACTION3A307 - 335
4X-RAY DIFFRACTION4B85 - 170
5X-RAY DIFFRACTION5B171 - 263
6X-RAY DIFFRACTION6B264 - 335

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more